Mercurial > repos > iuc > fastp
diff fastp.xml @ 6:a935cbdf1c0e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
| author | iuc |
|---|---|
| date | Thu, 23 Aug 2018 02:53:34 -0400 |
| parents | 3e2551a37201 |
| children | 6c2351178f8d |
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--- a/fastp.xml Fri Aug 10 19:40:07 2018 -0400 +++ b/fastp.xml Thu Aug 23 02:53:34 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.2"> +<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.3"> <description>- fast all-in-one preprocessing for FASTQ files</description> <macros> <import>macros.xml</import> @@ -154,7 +154,7 @@ #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x': $read_mod_options.polyx_tail_trimming.polyx_trimming_select - #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len): + #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len): --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len #end if #end if @@ -260,7 +260,7 @@ <!-- Read Modification Options --> <section name="read_mod_options" title="Read Modification Options"> <conditional name="polyg_tail_trimming"> - <param name="trimming_select" type="select" label="PolyG tail trimming" help="Useful for NextSeq/NovaSeq data"> + <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records."> <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option> <option value="-g">Force polyG tail trimming</option> <option value="-G">Disable polyG tail trimming</option> @@ -444,6 +444,15 @@ <param name="poly_g_min_len" value="10"/> <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/> </test> + <!-- Ensure polyX trimming works --> + <test expect_num_outputs="2"> + <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/> + <param name="single_paired_selector" value="single"/> + <param name="trimming_select" value="-G"/> + <param name="polyx_trimming_select" value="-x"/> + <param name="poly_x_min_len" value="10"/> + <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/> + </test> </tests> <help><![CDATA[ .. class:: infomark